Table 2.
Ten most significant VMRs identified in the MCCS and their respective ranking in TCGA
| MCCS | TCGA | |||||
|---|---|---|---|---|---|---|
| Genomic location of the VMRs (GRCh37) | minfdr* | Number of CpGs | Associated gene | Genomic location of the VMRs in relation to the corresponding genes | minfdr* | Rank in TCGA |
| chr20:13199787–13201844 | 5 × 10−181 | 29 | ISM1 | TSS1500 | 1 × 10−120 | 10 |
| chr5:112073348–112074043 | 5 × 10−181 | 16 | APC | Body, 1st exon, TSS200, TSS1500 | 3 × 10−170 | 4 |
| chr17:42091713–42093050 | 4 × 10−172 | 16 | TMEM101 | TSS1500, TSS200, 5′UTR, 1st exon | 3 × 10−92 | 20 |
| chr11:2290953–2293552 | 2 × 10−152 | 41 | ASCL2 | 3′UTR, 1st exon, 5′UTR, TSS200, TSS1500 | 1 × 10−90 | 23 |
| chr10:134598496–134602228 | 1 × 10−142 | 39 | NKX6 | Body, 1stExon, TSS1500 | 6 × 10−118 | 12 |
| chr1:228644750–228647248 | 1 × 10−131 | 28 | HIST3H2A/HIST3H2BB | TSS1500, TSS200 | 2 × 10−196 | 2 |
| chr6:29973557–29976071 | 4 × 10−124 | 52 | HCG4P3/HLA-J | Body | 2 × 10−194 | 3 |
| chr1:2460621–2462364 | 1 × 10−110 | 11 | HES5 | 3′UTR, Body, TSS200, TSS1500 | 3 × 10−90 | 24 |
| chr10:11059290–11060652 | 2 × 10−109 | 14 | CELF2 | TSS1500, TSS200, 5′UTR, 1st exon | 9 × 10−130 | 7 |
| chr12:3862221–3862810 | 6 × 10−104 | 13 | EFCAB4B | 1stExon, 5′UTR, TSS200, TSS1500 | 7 × 10−198 | 1 |
*minfdr: minimum adjusted P-value, TSS200 is the region from Transcript start site (TSS) to 200 nucleotides (nt) upstream of TSS; TSS1500 is the region from 200 to 1500 nt upstream of TSS; 5′ UTR is the region within 5 prime untranslated region, between the TSS and the ATG start site; body is the region between the ATG and stop codon; 3′ UTR is between the stop codon and poly A signal